DNA TOPOLOGY TWIST AND WRITHE

 DNA topology describes the coiling of a molecule of DNA

 Each of the chromosomes of the eukaryotes is comprised of a single linear DNA molecule.
Because their ends are free, linear DNA molecules can freely rotate to change the number of
times the two chains of the double helix coil about one another.
 However, DNA molecules can also be circular. Examples of circular DNA molecules include
most bacterial chromosomes, some viral chromosomes and small bacterial genetic elements
called plasmids. For such covalently closed circular DNA, the absolute number of times the
chains coil about one another cannot change. These DNA molecules are said to be
topologically constrained.
 Even the linear DNA molecules of eukaryotic chromosomes can be topologically constrained
because of their interactions with other cellular components.
 Since each of the two strands of the covalently closed circular DNA (cccDNA are covalently
linked circular chains, and because they coil around one other, the strands cannot be
separated from each other without breaking a covalent bond and opening the circle of one
of the strands. The two strands could be separated, if they were able to magically pass
through each other. The number of times one strand would have to be passed through the
other strand in order for the two strands to be entirely separated from each other is called
the linking number.
 The linking number is always an integer. The linking number is an invariant topological
property of a cccDNA. No matter how much a cccDNA molecule is distorted, the linking
number remains constant. The linking number is the sum of two geometric components
called twist and writhe.
 Twist is simply the number of helical turns of one strand about the other. In other words, the
twist number is equal to the number of times one strand crosses in front of the other strand.
If cccDNA is lying flat in a plane, the linking number is equal to the twisting number.
 If the twists form a right- handed helix, as in DNA under normal conditions, they are given a
positive twist number. To determine if the helix is right- handed, think of it as a screw. a
right- handed screw should be twisted to the right, clock- wise, to screw it into a board. Also,
in a right- handed helix, the strand in front at a cross- point is pointed up to the right.
 If the twists form a left- handed helix, as can occur under special circumstances, they are
given a negative twist number. A left- handed screw should be twisted to the left, counter-
clockwise, to screw it into a board. Also, in a left- handed helix, the strand in front at a cross-
point is pointed up to the left.
 However, cccDNA does not generally lie in a flat plane. Instead, the DNA double helix usually
crosses over itself in three- dimensional space, often repeatedly. This torsional distortion is
called writhe.
 Writhe can take two forms. One form is interwound or plectonemic writhe. In interwound
writhe, the DNA is wound around itself, forming a helix. Most cccDNA molecules exhibit
interwound writhe.
 The writhing number is the total number of writhes in a molecule of DNA. If right- handed
DNA forms a right- handed interwound helix, the DNA must twist to accommodate the
writhes. Therefore, right- handed interwound turns are assigned negative writhing numbers.
 Note that although the linking number must be an integer, the twist and writhing numbers
can have fractional values.
 If right- handed DNA writhes to form a left- handed interwound helix, the twist number of
the DNA decreases. Therefore, left- handed interwound turns are assigned positive writhing
numbers.
 The other form of writhe is spiral or a toroidal writhe. In spiral writhe, the DNA winds as if
around a cylinder. The spiral writhe often occurs when DNA molecules wrap around
proteins.
 If right- handed DNA writhes to form a right- handed spiral coil, the twisting number
decreases. Therefore, right- handed spiral turns are assigned positive writhing numbers.
Note that this is the opposite of right- handed interwound turns.
 If right- handed DNA writhes to form a left- handed spiral coil, the DNA must twist to
accommodate the writhe. Therefore, left- handed spiral turns are assigned negative writhing
numbers. Again, this is the opposite of left- handed interwound turns.
 Under normal physiological conditions, the average structure of DNA has about 10.5 base
pairs per turn of the helix. Therefore, the linking number of fully relaxed DNA can be
calculated by dividing the total number of base pairs by 10.5, to find the number of twists.
This linking number is assigned the symbol Lk0.
 If writhes are introduced into the DNA without changing the number of twists, the linking
number changes. The difference between the actual linking number and Lk0 is the linking
difference. If the linking difference is significantly less than zero, the DNA is negatively
supercoiled. If the linking difference is significantly greater than zero, the DNA is positively
supercoiled.
 cccDNA from both bacteria and eukaryotes are usually negatively supercoiled. Negative
supercoils can be thought of as a store of negative free energy that aids in the strand
separation for the processes such as DNA replication and transcription. When right- handed
interwound turns in the DNA are relaxed, the twist number decreases and the DNA unwinds.
 DNA molecules with the same sequence and length but different linking numbers are called
DNA topoisomers, since they differ only in topology. Topoisomerases are enzymes that
change the linking number of a DNA molecule.
 There are two types of topoisomerases. Type I topoisomerases increase the linking numbers
in steps of one. By introducing an additional twist, type I topoisomerases relax negative
supercoils.
 Type II topoisomerases change linking numbers in steps of two. Type II topoisomerases
require energy from ATP hydrolysis for their action. By changing the handedness of turns,
type II topoisomerases change the topology of DNA molecules.
 Prokaryotes have a special type II topoisomerase called DNA gyrase. DNA gyrase decreases
linking numbers in steps of two. DNA gyrase is responsible for the negative supercoiling of
chromosomes in prokaryotes.

Conclusion

 The linking number for a strand of covalently closed, circular DNA is constant. cccDNA
molecules with the same sequence but different linking numbers are topoisomers.
 The twist number is equal to the number of times one strand of cccDNA crosses in front of
the other strand. If the twists form a right- handed helix, they are given a positive twist
number. If the twists form a left- handed helix, they are given a negative twist number.
 The writhing number is equal to the number of times the double helix crosses over the long
axis of the double helix in three- dimensional space. The two forms of writhe are interwound
writhe and spiral writhe.
 cccDNA can be relaxed, positively supercoiled, or negatively supercoiled. cccDNA from both
bacteria and eukaryotes are usually negatively supercoiled. The negative supercoils are used
by the cell to help unwind DNA.
 Cells use topoisomerases to change the linking numbers of cccDNA molecules. Type I
topoisomerases increase the linking numbers one step at a time, while type II
topoisomerases change the linking numbers two steps at a time.